Pawel Swietach - Cell physiology Metabolism & Endocrinology 'Break the Acid Cycle: Targeted Collapse of Tumour Adaptation'

Guided by Darwinian modelling and breakthroughs in understanding adaptive mechanisms, we will develop tools that cause cancer cells to succumb to their own metabolic products, making tumours more vulnerable to therapies.

Key references:

• How protons pave the way to aggressive cancers. Swietach P, Boedtkjer E, Pedersen SF. Nat Rev Cancer. 2023 Oct 26. doi: 10.1038/s41568-023-00628-9
• CRISPR-Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH. Michl J, Wang Y, Monterisi S, Blaszczak W, Beveridge R, Bridges EM, Koth J, Bodmer WF, Swietach P. Cell Rep. 2024 Jul 23;43(7):114499. doi: 10.1016/j.celrep.2024.114499. Epub 2024 Jul 2.
• Acidosis attenuates the hypoxic stabilization of HIF-1α by activating lysosomal degradation. White B, Wang Z, Dean M, Michl J, Nieora N, Flannery S, Vendrell I, Fischer R, Hulikova A, Swietach P. J Cell Biol. 2025 Aug 4;224(8):e202409103. doi: 10.1083/jcb.202409103. Epub 2025 Jun 24.
• Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance. Michl J, White B, Monterisi S, Bodmer WF, Swietach P. Proc Natl Acad Sci U S A. 2024 Mar 26;121(13):e2319055121. doi: 10.1073/pnas.2319055121. Epub 2024
• Acid-adapted cancer cells alkalinize their cytoplasm by degrading the acid-loading membrane transporter anion exchanger 2, SLC4A2. Michl J, Monterisi S, White B, Blaszczak W, Hulikova A, Abdullayeva G, Bridges E, Yin Z, Bodmer WF, Swietach P. Cell Rep. 2023 Jun 27;42(6):112601. doi: 10.1016/j.celrep.2023.112601. Epub 2023 Jun 3.

 According to simulations of somatic evolution, malignant growth could be stably disrupted by blocking survival adaptations to cancer-generated selection pressures which are otherwise toxic. Certain chemical features of the tumour microenvironment are harsh, therefore successful cancer phenotypes must adapt. Blocking a vicious cycle is intuitive, but there is a paucity of targets for cancer therapies. Not all adaptive responses fit the criteria; for example, HIF-driven adaptations to hypoxia reduce oxygen consumption and weaken the hypoxic selection pressure. A process that meets the criteria is the adaptation to tumour acidosis because acid-resistance, acquired through upregulating respiratory flux, maintains acid-production (as CO₂). If targeted effectively, this cascade presents therapeutic potential. Establishing experimental evidence for an anti-tumoural outcome would verify a key prediction in cancer physiology.

We are well placed to address this challenge in colorectal cancer. Firstly, our CRISPR/Cas9 screen listed essential genes for surviving acidosis, notably NDUFS1 and related respiratory genes. This identifies a mechanism to inhibit. Secondly, we associated acid-resistance with surface-expressed glycoproteins CEACAM5 and CEACAM6. This defines an accessible molecular signature to target. Thirdly, we developed tuneable ionophores that block respiration and refined self-assembling lipid cubosomes for protecting and delivering such payloads. This marks a substantial advance over previous approaches to block mitochondria (e.g., Metformin).

Our proposal presents a complete strategy for targeting acid-adaptation, informed by our collective expertise in physiology, drug design, and nanoparticle delivery. We will refine next-generation ionophores that target mitochondria more selectively, beginning from our lead-compounds and guided by structure-activity relationships. Uniquely, our compounds produce steeply cooperative dose-response curves, resulting in low toxicity at low concentrations but near-complete killing at modestly higher concentrations. To attain the desired outcome, we propose to concentrate the ionophore in acid-resistant cells using cubosomes for protection and delivery. To that end, we will optimise cubosome composition alongside modifications to ionophore design, using cryo-EM and dynamic light scattering to verify structure, high-performance liquid chromatography to quantify loading, and glycolytic stimulation and cell killing assays as acute and long-term readouts of drug efficacy. To target acid-resistant cells residing in acidic niches, cubosomes will be functionalized with binders to CEACAM5/6. To improve precision and reduce systemic toxicity, synthetic nanobody binders (sybodies) will be screened in vitro for preferential binding to protonated CEACAM5/6: the dominant conformational state in acidic tumour niches. Binder-functionalized, ionophore-loaded cubosomes will be tested for acute respiratory inhibition and long-term killing efficacy in acid-resistant and acid-sensitive colorectal cancer cell lines, selected from our panel of 70.  Products that selectively kill acid-resistant phenotypes will be tested for efficacy in vivo using murine xenograft admixtures of fluorescently-labelled acid-resistant and acid-sensitive lines. Histological analyses will decipher changes in the phenotypic landscape.

We postulate that inactivating acid-driven selection in colorectal cancer can disarm disease progression by eliminating acid-resistant cells, a phenotype incentivised to secrete acidic metabolites in a bid to out-compete acid-sensitive neighbours. Eliminating acid-adapted, respiring cancer cells could improve oxygen availability for radiotherapy. By stably reducing tumour acidity, our intervention could improve host defences and disinhibit immune-cell therapies. The novel research tools (binders, ionophores, nanoparticles) will advance our understanding of the biological significance of tumour acidosis, unravelling therapeutic and diagnostic opportunities.